A DNA origami plasmonic sensor with environment ......A DNA origami plasmonic sensor with...

Electronic Supplementary Material

A DNA origami plasmonic sensor with environment-independent read-out Valentina Masciotti1,2 (), Luca Piantanida1,†, Denys Naumenko1,3, Heinz Amenitsch4, Mattia Fanetti5, Matjaž Valant5,6, Dongsheng Lei7,8, Gang Ren7, and Marco Lazzarino1 ()

1 CNR-IOM, AREA Science Park, Basovizza Trieste I-34149, Italy 2 PhD Course in Nanotechnology, University of Trieste, Trieste I-34127, Italy 3 Institute for Physics of Semiconductors, National Academy of Sciences of Ukraine, Kyiv 03028, Ukraine 4 Institute of Inorganic Chemistry, Graz University of Technology, Graz A-8010, Austria 5 Materials Research Laboratory, University of Nova Gorica, Nova Gorica SI-5000, Slovenia 6 Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, China 7 The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley CA 94720, USA 8 School of Physical Science and Technology, Electron Microscopy Center of LZU, Lanzhou University, Lanzhou 730000, China † Present address: Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA Supporting information to https://doi.org/10.1007/s12274-019-2535-0

Index 1. The design 2. Purification and additional characterization 3. AFM analysis of the kite-like DNA origami 4. Additional SEM and TEM and Cryo-EM characterization 5. SAXS data 6. LSPR analysis

6.1 LSPR measurements in liquid 6.2 LSPR measurements in gel and data treatment

7. Table of nucleotide sequences References

1. The design Each edge of the wireframe DNA origami tetrahedron is composed of four dsDNA helix ~90 nm long and is connected to the other two neighboring edges at the vertices by flexible joints. The scaffold strand, coming out from the struts, crosses each vertices twice. The connection points between the struts are composed by 5 bases left at single strand. The number of bases composing three of the six struts slightly differ to fold completely the scaffold strand. Three of the struts have been designed with a central seam which separates the two half of the pillar itself, so we properly prolonged the staples strands tuning their pairing to build a cage around the seam in order to reinforce the central part. In the three pillars left, the scaffold strand still forms a central seam but the external helix extends along the entire length of the pillar maintaining the struts more robust (Fig. S1).

Figure S1 Visual model of the scaffold strand folding path: six 4-helix bundles in blue, the flexible connections at the vertices in red. There are two different types of struts: the two half struts typology and the strut with a central seam. On the right side, a focus of the vertex connection.

Address correspondence to Valentina Masciotti, [email protected]; Marco Lazzarino, [email protected]

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Two different sets of staples fold the two struts involved in the probe-target actuation facet: (i) staples pair the entire scaffold strand of the struts (0ss), (ii) staples leave unpaired 4 nucleotides of three helices of the struts (3ss) (Fig. S2). The purpose was to plan two different tetrahedral DNA origami characterized by different mechanical properties.

Figure S2 Two set of staples containing: no single strand (0ss) and 4-single strands bases in 3 helices (3ss). The scaffold strand is blue, the structural staples strands are red, the staples involved in the variable part of the struts are grey, and the green dotted segments are the 4-bases gaps where the scaffold strand is left unpaired. On the right, the arrows indicate the position and the number of weak points.

0ss and 3ss have been separately designed through the help of design-assisted software caDNAno; the list of nucleotide sequences of staple strands, catchers strands, probe and target are shown in section 7.

2. Purification and additional characterization The purification of the folded structure from excess of staples strands has been initially operated through Amicon filtration. In Figure S3(a) is shown an UV image of agarose gel: in the first and in the third lanes we can observe the migration of the ladder and of the M13mp18 while the forth and the fifth wells were filled with DNA origami tetrahedron respectively before and after the Amicon purification. The red box in Figure S3(a) identifies the gel bands corresponding to the well folded origami. As expected, after the purification step the staples were removed and the origami concentration was increased (band brightness enhancement). Meanwhile we witnessed to the formation of two slower bands which correspond to larger constructs, probably derived from the aggregation of two and three tetrahedrons. SEM characterization confirmed the agarose gel indications: most of the tetrahedrons analyzed were aggregated (Fig. S3(b),(c)) or broken in different places, probably because of the harsh purification step. These results suggested that the purification of the DNA origami tetrahedron with Amicon was not successful; for this reason no staple purification has been used in all the performed experiments.

The DNA origami concentration was calculated using ImageJ software: the brightness of the whole lane can be assumed proportional to the M13mp18 initial concentration (10 nM), so the ratio between the brightness of the origami band and of the entire lane is equivalent to the ratio between the concentration of the scaffold strand and of the origami tetrahedron. SEM analysis did not highlight structural differences among 0ss and 3ss tetrahedrons.

Figure S3 (a) Agarose gel electrophoresis of DNA origami tetrahedron shows the concentration and the aggregation enhancement after Amicon purification, M13mp18 is used as a control of the folding success; (b) and (c) SEM pictures in which there are well-folded tetrahedron, broken and aggregated DNA architectures.

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The anchoring of AuNP to the DNA origami was extrapolated from agarose gel analysis: first we calculated the DNA origami concentration from the fluorescence intensity of well folded DNA origami band compared to the intensity of the entire lane as described above. Since the total amount of M13 in the sample was 6.25 nM and we loaded 10 μl in each well of the gel we can estimate the concentration of well folded DNA origami present in the bands of interest. In the same way we calculated the AuNP absorbance and we obtained the ratio between the absorbance in the band of interest and the entire lane. Since the initial concentration of AuNP was 6.25 nM, the ratio AuNP: M13 is 1:1 while the ratio AuNP: well folded DNA origami tetrahedron is 4:1. Since the band of interest may contain tetrahedron without AuNP, tetrahedrons with only one AuNP, and tetrahedron correctly formed with 2 AuNP, we further needed to evaluate the relative probability of these three configurations. We analyzed 220 DNA origami from 50 SEM pictures and we found out 115 structures with AuNP dimers, 105 structures with a single AuNP: therefore, we assumed a ratio between dimer and single NP of 1:1.

Finally, from the gel presented in Figure 1 the yield of dimers obtained was (1) 13% for 0ss, (2) 8.3% for 0ss+Target, (3) 10% for 3ss and (4) 10% for 3ss+Target.

3. AFM analysis of the kite-like DNA origami AFM analysis was performed in contact mode in air [S1, S2], on the “kite-like” DNA origami and we observed that that almost all the structures were in the flat configuration, except few of them which were folded on themselves (Fig. S4(a)), probably because the scaffold strand can still pull the two halves of the broken strut together. Moreover, the flexibility of the vertices provides enough degrees of freedom to allow the folding of the structure on itself even if it is statistically less probable, due to the electrostatic repulsion between the origami struts. The profile of the kite-like DNA origami deposited on mica as measured from the topographic images, post-processed with Gwyddion software, highlights an average strut height of 2 nm which is substantially lower than 2 double-helix value in solution (between 4 and 5 nm) (Fig. S4(b),(d))[S3]. Numerically the same results were obtained also in tapping mode in liquid but with a lower image quality. These discrepancies are often observed when imaging in air with AFM because of a combination effects of water drying and AFM tip pressure, therefore these measurements are usually considered only indicative [S4]. The apparent width of the dsDNA molecules is strictly correlated with the tip used, but it was always exceeding the 2 dsDNA diameter in solution, which is to be expected for tips with apex radii exceeding substantially the molecular diameter (Fig. S4(c)).

Figure S4 (a) AFM image of the flat version of tetrahedral DNA origami, few of them are folded on themselves; (b) height profile of the structures shown in Figure 3.1(a); (c) width of the kite-like struts using Gwyddion tool; (d) 3D AFM image of a kite-like DNA origami.

4. Additional SEM and TEM and Cryo-EM characterization Transmission electron (TEM) and cryo-electron microscope (cryo-EM) have been used in combination with scanning electron microscope (Fig. 1(d)) to validate the folding of the tetrahedron (Fig. S7).

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Figure S5 TEM images representing the well-folded tetrahedron shown in Figure 1(d) (scale bar 50 nm).

Figure S6 DNA origami tetrahedron conjugated with one AuNP: on the left SEM image with a broken tetrahedron in which is visible the right AuNP positioning; on the right cryo-EM of a broken tetra with one AuNP confirmed the central positioning of the AuNP in one AuNP facet.

In order to selectively decorate the DNA origami structure with one or two gold nanoparticles, we initially synthesized it using only one set of catchers strand which are involved in the binding of one AuNP.

The conjugation of one AuNP to the DNA tetrahedron, still allows to visualize the tetrahedral shape. Moreover, the presence of kite-like structure, as in Figure S6, evidences the precise positioning of the AuNP in the center of a tetrahedral facet.

Further functionalization with the second gold nanoparticles has been performed through the addition in the DNA origami synthesis mix of another set of catcher strands, recognizing the same AuNP functionalization. The presence of a second NP attached to the tetrahedral architecture, further increases the signal background, coming from secondary electrons scattered by the two nanoparticles, thus outshining the signal generated by the origami itself. In some cases, the triangular shadow, attributable to DNA origami, can be still observed (Fig. S7).

Figure S7 Dimers of gold nanoparticles with a triangular like shadow representing DNA origami tetrahedron with two gold nanoparticles (Scale bar 100 nm).

Cryo-EM characterization (Fig. S8) showed triangular like structures heterogeneously distributed in the grid, often anchored to the lacey carbon film formed net. Nonetheless, it is still possible to appreciate the presence of many AuNP dimers deriving from tetrahedrons not clearly distinguishable.

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Figure S8 Cryo-EM images of dimers of gold nanoparticles with a triangular like DNA origami structures; in the second picture it is possible to appreciate that the hybrid AuNP-DNA origami structures are heterogeneously dispersed in close proximity of the lacey carbon film formed net (Scale bar 50 nm).

5. SAXS data In order to facilitate the comparison between the SAXS pattern before and after the structure factor derivation in Figure S9 is shown the zoom of the data presented in Figure 2(a) and (b) restricted to the q-range of interest.

Figure S9 Zoom in the q-range of interest of SAXS data presented in Figure 2(a) and (b)in the main text. (a) Scattering pattern of all samples and the DNA- functionalized AuNP reference sample do not present significant peaks in the region of interest since the signal is mainly dominated by free AuNP in solution; (b) to extract the particle-particle interference, the structure factor has been derived by dividing the pattern with the AuNP signal (gold-yellow line). The structure factor of the different tetrahedrons highlights the presence of differences only between 3ss before and after target hybridization while no relevant variability has been recorded in 0ss structures after target addition.

6. LSPR analysis A basic equation to calculate the actual extinction spectra is:

A + S + R + T = 1 (1) where A is absorption, S is scattering, R is reflection and T is transmission of the light and A+S= E represents the extinction. Neglecting the difference in the light reflection from the surface of clean gel and the one with AuNP, E = 1- T. Thus, the final equation to calculate the extinction is:

E = (I0-Ii)/(I0-Ibg) (2) where Ii is the corresponding intensity of light passed through each band, and I0 is the intensity of light passed through the clean gel in a position without origami and nanoparticles. Ibg is a dark thermal noise of CCD. At least 5 different positions along each band have been characterized and finally averaged [S5].

6.1 LSPR measurements in liquid

The measurements in liquid have been performed in a home-made cell fabricated from a PMMA slab with two coverslip glasses attached to both sides. 10 μl of liquid sample was loaded in the chamber preliminary created in the slab avoiding the formation of air bubbles.

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Figure S10 Extinction spectra of AuNP-tetrahedral DNA origami in solution before and after the probe-target actuation of 0ss and 3ss respectively demonstrating that LSPR shift cannot be observed. In both samples the target addition does not shift the plasmon resonance for the contribution of free AuNP dominating the spectra, as discussed in the main text. However, we observed that in both cases after the target addition the resonance width decreases, as a consequence of the greater stability conferred to the structure by the hybridized probe, and the subsequent reduction of thermal fluctuations.

6.2 LSPR measurements in gel and data treatment

The extinction spectra show a peak in the range of 525-535 nm which is attributed to the LSPR in single gold AuNP or dimers. The spectra in gel demonstrate a different extinction at short wavelengths complicating an estimation of LSPR position. Since the gel density, gel hydration and AuNP size in each series of experiments are supposed to be constant the difference in the extinction is caused by a variable gel thickness of the lanes.

The best agreement between the experimental data for single DNA-coated AuNP in liquid and simulations was obtained with εeff = 2.0 which in terms of effective medium approximation (EMA) corresponds to εeff = 0.34∙εDNA + 0.66∙εwater, where εDNA = 2.450 and εwater = 1.769 are dielectric permittivity of DNA and water respectively. The εeff in gel increases by 1% since dielectric permittivity of gel is higher than of water (εgel = 1.796). The experimental data displayed in Figure 3(c) were fitted with 2 Gaussian curves (Fig. S11), each of them represents the particular extinction process and is related to: i) plasmon excitation in AuNP dimer, ii) variation in gel thickness and/or structure. The first term was fully variable while the wavelength position and the peak width of the second were fixed and obtained from the measurements of clean gel (Fig. S12). Notice that the peak height was variable in the second case.

Figure S11 it procedure. The experimental data of 3ss-AuNP hybrid structure without and with target displayed in Figure 3(c) were fitted with 2 Gaussian curves, each of them represents the particular extinction process and is related to: plasmon excitation in AuNP dimer (green curve), variation in gel thickness (red curve).

Figure S12 The image below represents a fit of the gel spectrum with one Gaussian function. Its peak position will be fixed at 475 nm, a width at 160 nm, while a height will be variable.

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7. Table of nucleotide sequences

Table S1 List of the nucleotides sequences used for the synthesis of the DNA origami tetrahedron structures (ST). The catchers strand for the anchoring of AuNP positioned in the facet 1 and 2 are named 1NP and 2NP: the black sequence is complementary with the structure sequence, while the green sequences represents the region complementary to the AuNP sequence and the red part in the linker. The catchers for the actuator strand and the actuator strand. Two different sets of staples strand have been used for the synthesis of the DNA origami tetrahedron 0ss and 3ss.

NAME Sequence 5' ----->3' Length (nt)

ST1 AAATCAAATTTAATTGACGGTGTCTGGAAGTT 32

ST2 ATAGCCGAACAGAGATGGTTTA 22

ST3 GTAAAGCACAAGTTTTCCAACGTCAAAGGGCG 32

ST4 ACCACATTGATAGCGTCTAATGCAGAACGCGC 32

ST5 TGCCTGCAACAACATAGGCGCCAGGGTGGTTT 32

ST6 CGTATTAATTCCGAAAGACGGGGAAAGCCGGC 32

ST7 ACCACCGGATCAAAATGAACAAGATGATATTC 32

ST8 CTAAATCGTTTTGCGGCTCAGAGC 24

ST9 AAGGGAACTAAAACGACTTATTACGCAGTATG 32

ST10 TTCTTTTCTGGGTTATCTAGAGGATCCCCGGG 32

ST11 AGTGTACTGGTAATAAGTT 19

ST12 GAATTGAGAGCCGTTTACAGCCATATTATTTA 32

ST13 AAATTCTTCAATAGGATTCCGGCA 24

ST14 CTTGCTTCAATCAATAATTTCAATTACCTGAG 32

ST15 CTCATTTTGTCAATAAAAACAAGA 24

ST16 GGCAATTCTAAGACGCGTAGATTTTCAGGTTT 32

ST17 ATAAGAATAAATGTGAGCATCTGCCAGTTTGA 32

ST18 TATTACAGCTGAATATGTAATTCTGAATCCCC 32

ST19 TAACTCACCGCCAGGGAAATATATTTTAGTTA 32

ST20 ACAAACAAGTCAGACGCCCTCAGAGCCGCCAC 32

ST21 GTAAATATAAATGAATCGCCCACGCATAACCGATA 35

ST22 CACTAACAACAGTTGACAGCAAGCGGTCCACG 32

ST23 TCAACATTAAACACCGTGTTGGGAAGGGCGAT 32

ST24 TCACCCTCGCTTGATAACAGTTTCAGCGGAGT 32

ST25 ATTTCATCAGTCGGGACGTTGCGCTCACTGCC 32

ST26 GCTGATGCGCGTATTGCGAGCCGGAAGCATAA 32

ST27 ATTTGGGAATACATGGCAAGTTTGCCTTTAGC 32

ST28 TTTAAAAGCCCCAGCAGAAGGGAAGTCAGTTG 32

ST29 CTTTACAATAGAGCTTTCGGCAAAATCCCTTA 32

ST30 TAAAACGAATGTTCAGCCAATACT 24

ST31 AACAATGAAAACCAAGAAACGATTTTTTGTTT 32

ST32 TTAGACTGCAACTAATGAAAAATCTACGTTAA 32

ST33 GCCAGTAAACTAAAGTCTCCTTTTGATAAGAG 32

ST34 TAATTAATTTTCCCTTTGAATTACAACAAACATCAAGAAA 40

ST35 AGTACATATGTAAATCAATAACGGATTCGCCT 32

ST36 TAAATCAATCTATCAGCACTACGTGAACCATC 32

ST37 GGGGACGATGCGCAACGAATCATAATTACTAG 32

ST38 CAATTCTATAAATTGTTAATCAGAAAAGCCCC 32

ST39 GCCAGTTAGAGCAAGATAAATATAACCCACAA 32

ST40 TTTTCATAAACCGCCTATTGGCCTGTCCACTA 32

ST41 GGAATAAGTTTTTTCAGGAGCCTTTAATTGTA 32

ST42 GAATTAGCAAAATTAAGATAAAAAGCCGGAGAACCGCCAC 40

ST43 GCTTAGATATCAATATGTTTGGATTATACTTC 32

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ST44 AGAGTACCAATCAGGTGCAGAGGCATTTTCGA 32

ST45 GCAGGGAGACAACCATTTTCTGTATGGGATTT 32

ST46 AATTCATAAAAGGAACCTTTCGAGGTGAATTT 32

ST47 ACCCAAATCTAAATCGCCCGAGAT 24

ST48 CACCAACCCGAACTGATTACCCAAATCAACGT 32

ST49 CGACGATAAAAACCAAACCCTCGTTCATTGTGAATTACCT 40

ST50 AATCATTATGAAGCCTTTAGTTGCTATTTTGC 32

ST51 CCTCAGAATACCGCCAGCCTCAGAGCATAAAG 32

ST52 AAGAACCGCGTAGAAAAATGCCACTACGAAGG 32

ST53 CACCAGAGCAGTCTCTTTTTCATCGGCATTTT 32

ST54 GCCCGTATATAGTTAGTGCTCAGTACCAGGCG 32

ST55 CTGCCTATCCATGTACACAACGCCAGGGTTGATATAAGTA 40

ST56 CATTTCGCTATAAAGCGAAAGACT 24

ST57 GCGCATAGAAAAAAGGTTTTTCATAACGCAAAGACACCAC 40

ST58 CAAAAGAAGGAGAAACGTCGCTAT 24

ST59 CACTAAAAAACGAGGCCAGTGAATAAGGCTTG 32

ST60 CCAACATGTATAACAGAACAGGTCAGGATTAG 32

ST61 TTTGTCGTGGGGTCAGCCTCAAGA 24

ST62 TAGTCAGCAAACTCCTTGATTCCCAATTCTG 31

ST63 TCCCAATCAAGTCAGAAATAATAAGAGCAAGA 32

ST64 CAGCCCTCAAACAGTTCTGAAACATGAAAGTA 32

ST65 GATTGCTTAATTATTCTATGTGAGCTAAGAAC 32

ST66 ATTCAGGCCGACAGTACTGTAGCCAGCTTTCA 32

ST67 GCTTAGGTACCAGTGAATTGTTATCCGCTCAC 32

ST68 GCGAAAGGGGATAGGTACAAACGGCGGATTGA 32

ST69 CAATAATCGGCTAAGAAAAGTA 22

ST70 CCTGAACACAAATAAGTACCGCACTCATCGAG 32

ST71 GTCAGACTGCCAAATCCAGCAACCAGAACCAC 32

ST72 GAAAAATATTTAAGAACATAGTAAGAGCAACA 32

ST73 AATAATAATTTATTTTACAGAGGCTTTGAGGA 32

ST74 ATTTCATTAGAATCCTACAGTAACAGTACCTT 32

ST75 TGAGGCAGATAAATCCATTAGCGTTTGCCATC 32

ST76 TTCATTTGCGCATTAAACTAGCATGTCAATCA 32

ST77 GACGACAATAAACAACACTAACGGGTTGAGATTTAGGAAT 40

ST78 ATATCAGACAAAATAATTATTTTCATCGTAGG 32

ST79 CAGACGTTAGTTGACGGAAATT 22

ST80 AATTCCACGGTCGACTATAACTATATGTAAAT 32

ST81 GGAGGTTTCCGCGCCCTTCCAGAGCCTAATTT 32

ST82 AACGTCAGAATTGATTAATCCTACATTTAACA 32

ST83 GCAAGGCAATAAACCCTCAGACAGTCAAA 29

ST84 TGATAAATGAAAGTAAGCCTGGATTGTATAAG 32

ST85 TCTAAAATATCTTTAGGAG 19

ST86 AAAAACAGTAATGCCGAGTAGCATTAACATCC 32

ST87 CAGAGGCGTGAATACCCCGGTATTTGAATAAC 32

ST88 GAAATAAAGGAAGGGTCTGATTATCAGATGAT 32

ST89 TTACATCGGATGATGACTTTTTTAATGGAAAC 32

ST90 GATGGTGGATCCTTTGATTTAGAAGTATTAGA 32

ST91 GTATCATCGCCTGATAAAT 19

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ST92 CCCTGACGAATAACGGTTTGACCCCCAGCGAT 32

ST93 CCTGAGAGATCGTAAAATTTTTGTTAAATCAG 32

ST94 GGCGGTTTAAATCCAACAGTGCCAAGCTTGCA 32

ST95 AGGGCGACAACTTTCACCGATAGTTGCGCCGA 32

ST96 GCCCTTTTTGTCTTTCATAGCAGCCTTTACAGAGA 35

ST97 ATGTTTTAAATATGCATAAGAGAAAAACGAGAATGACCAT 40

ST98 GATAATACCGAGAAAGGGCGAAAATCCTGTTT 32

ST99 AAGGTAAAAATGCTGTGCTTAGAG 24

ST100 ATCTCCAAGCTGGCTGATAAAAGAGAGGAAGTTTCCATTA 40

ST101 TAAGCGTCATTAGAGCACCAGTAGCACCATTA 32

ST102 GAAGGATTAGGATTAGCTGAGACTTGCCTTGAGTAACAGT 40

ST103 GGCATGATTGCTCATTGCAGACGGTCAATCAT 32

ST104 CTGGTTTGTTTGAGTAATTAGAGCCGTCAATA 32

ST105 AACAAGCATTAAGCCCGGGTAATTGAGCGCTA 32

ST106 AGGGTTGAGTGTTGTTCGTGGACTTTGGGGTCCCAGAGCC 40

ST107 TTAAAATTGGGCGCGAGGCTATCAGGTCATTG 32

ST108 TGAATAATGAAATTGCTGAGAAGAGTCAATAG 32

ST109 AATAAATCAATGCAATTGTGTAGGTAAAGATT 32

ST110 TTAAGAGGCGGGGTTTCGTAACGATCTAAAGT 32

ST111 TGTAGAAAAACTTTAATTACCAGA 24

ST112 TCAAATATCGCGTTTTGGAAGCCCCAACGCTCAACAGTAG 40

ST113 CGGTCATACCGCCACCAGCATTGACAGGAGGT 32

ST114 ACGCTAACACAATTTTAACCTCCCGACTTGCG 32

ST115 AACGGGTAACGGTGTACAAGAGTAATCTTGAC 32

ST116 GTGCCAGCTGCATTAAACTTTTTCTTTTCCCA 32

ST117 GAATCGATGAACGGTATCTGGAGCCCTGTTTAGCTATATT 40

ST118 CTTAATTGGTAGAAAGTATTCATTGTCCAGAC 32

ST119 CGGGTATTAATAGCAAAGAATTAACTGAACAC 32

ST120 CGGAATTATCATCAAAATCATA 22

ST121 ATTATTTGCACGTAAAACA 19

ST122 ATCGATAGCAGCACCGTAA 19

ST123 TTGAGAGACCGGTTGAAAACGTTAATATTTTG 32

ST124 CAATGACATTAAAGGCGATTGAGGGAGGGAAG 32

ST125 ATATTTTAATACAGGCATTCAACCGTTCTAGC 32

ST126 AACGTCAATAGACGGGTAGCTATCTTACCGAA 32

ST127 GTCAGGACCAACAATAGGTAATAGTAAAATGT 32

ST128 CTAAAGACCTCCAAAACGTTGAAA 24

ST129 AACGCAATAGAAACACACCTGCTCCATGTTAC 32

ST130 TGAATTTATCATATTCTAGAACCTACCATATCAAA 35

ST131 CAAATATTCTAATAGTGAGAGGGTAGCTATTT 32

ST132 GAGGGTAGTCAGCTTGAACTAAAGGAATTGCG 32

ST133 CGCTTTCCTTCTGACCCTGCAAGGCGATTAAG 32

ST134 AAATACCGCCGTGGGACACGTTGGTGTAGATG 32

ST135 GGCAACATACCTTCATCAGACCAG 24

ST136 TCAGTAGCAAGGCCGGGTCACCGACTTGAGCC 32

ST137 CGGTGCGGGTAACCGTGCGAGTAACAACCCGT 32

ST138 CGAACGAGTGAGAATCCGGATTGCATCAAAAA 32

ST139 TGTGTCGAGCGCGAAAAGAAGGAAACCGAGGA 32

ST140 CCCCGATTACATGGCCGGCGAATTCGACAACT 32

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ST141 TATACCAAAATCCGCGCAGAACGAGTAGTAAA 32

ST142 CTTAAACAAGCAGCGACAGCGCCAAAGACAAA 32

ST143 GATAAGTGCTATTATTAATGCCCC 24

ST144 TTAAAGAACCAGTTTGCACCGGAAGAGGTGCC 32

ST145 GGAAAGCGCCGCCGCCCTCAGAGCCACCACCC 32

ST146 CCTCAGAAGCCCCCTTTCATTAAAGCCAGAAT 32

ST147 GAACAAAGGAGAGTTGAAGGAATTGAGGAAGGTTA 35

ST148 TCACCATCTGAGAAAGTTTTTAGAACCCTCAT 32

ST149 CGGATTCTACCGTGTGGCTATTACGCCAGCTG 32

ST150 AACAAAGCTAAGACTCAAGAGGCAAAAGAATA 32

ST151 CCTGGCCCTGAAAACCACCAGA 22

ST152 TCATTCCATAATTTAGCTTTACCCTGACTATTA 33

ST153 AAAAACCGAAGAATAGGAACCCTAAAGGGAGC 32

ST154 TTCGCGTCTGTTTAGTCAAAGCGCCATTCGCC 32

ST155 AAGCGCATAAATGAAACTTATCATTCCAAGAA 32

ST156 AAAAAGCCTGGCCTTCTCGGCCTCAGGAAGAT 32

ST157 CCGCTTCTGGTGCCGGAGCCAGCTACGCCATCAAAAATAA 40

ST158 TCAGAGCCGTAGCGCGGAATTTACCGTTCCAG 32

ST159 TACAAACTCGTAACACCAAGCCCA 24

ST160 GGCTTAATTAGATTTACTTCAAAGCGAACCAG 32

ST161 TGCTAAACATTCAACCCGCTTTTGCGGGATCG 32

ST162 GATTAAGAAATTCGAGGTTTGACCATTAGATA 32

ST163 GAACGTGGATTTGAGGCCCGAACGTTATTAAT 32

ST164 TATGCGATATATCCCAGAGGCTTTTGCAAAAG 32

ST165 TTGGGCTTAAGTTACCCAAAGTACAACGGAGATTT 35

ST166 TTGCCCTTGAGAGACTGTAATCAT 24

ST167 GCGAGGCGAGGCTTATAAGTTACATCTTACCA 32

ST168 TATGTACCTCTACAAAGCTGAAAAGGTGGCAT 32

ST169 AAGTTTTGTTACGAGGCTGGCTCATTATACCA 32

ST170 GAATAACATAAAAACAGGG 19

ST171 AAAAGGAACCAGAGGGGATAAGTCCTGAACAA 32

ST172 ACCGGAAGAAGCAAAGGCCATATTTAACAACG 32

ST173 CTGTTTATGTTGGGAAGCAGATACATAACGCC 32

ST174 CGCACTCCAAACCAGGATCATATGCGTTATAC 32

ST175 TTAGCCGGCACTCATCAATACCCAAAAGAACT 32

ST176 TCGGTTTACAACGGCTGTCACAATCAATAGAA 32

ST177 GGCGCATCGCCTCTTCATAAATAAGGCGTTAA 32

ST178 GGTCATAGCTGTTTCCTCGAATTCACCTTTTTAACCTCCG 40

ST179 ATAGGAACTTCGGAACCCGTCGAGTGTAGCATTCCACAGA 40

ST180 CCATTAGCGACAGAATCTTTTGATGATACAGG 32

ST181 GCGGAATCGTCATAAAATTCATCAAACAACAT 32

ST182 TATTCGGTCGCTGAGGCTT 19

ST183 ACAAAATTATGAATATTGAAAACATAGCGATA 32

ST184 TACCGAGCTGTGTGAAGACGGGCAACAGCTGA 32

ST185 GAGAATAGTGGTTTACAAGACAGCATCGGAAC 32

ST186 CTATCATAAATAGCGATCCTAATTTACGAGCA 32

ST187 GCAAATCAACTAATAGACATTATCATTTTGCG 32

ST188 TTAAAGGTGAATTATCACCAAACGTCACCAATGAAACC 38

ST189 TTAGCAAAGATATTCACCAACTTTGAAAGAGG 32

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ST190 GATATAGATTTTAGCGATCCTGAAAAATCGCG 32

1NP1 ACCCAGCTGAGCGTCTAATAGCAAGCAAATCAGTACTTCCTTAAACGACGCAGGCTTATCCTTCACGATTGCCACTTTCCAC

83

1NP2 CCGTAATGGGGATGTGTAAATTTAATGGTTTGGTACTTCCTTAAACGACGCCTTCACGATTGCCACTTTCCAC

73

2NP1 CAAAAGGGAATATGATAAGGCAAAGTACTTCCTTAAACGACGCCTTCACGATTGCCACTTTCCAC 65

2NP2 CTCAAATGCTTTAAACTGCGGATGAGCTCAACGTACTTCCTTAAACGACGCCTTCACGATTGCCACTTTCCAC

73

1NP3 GTCATTTTAGTTCAGATATAAAGTACCGACAAGTACTTCCTTAAACGACGCACTTCACGATTGCCACTTTCCAC

74

2NP3 ACAGATGAAAATACGTATACATACATAAAGGTGTACTTCCTTAAACGACGCAGGCTTATCCTTCACGATTGCCACTTTCCAC

83

CATCHER probe 1 TTGGGTAAATTAATTGAACCTGTCCTGCGAGCCCGGGAAGCT 42

CATCHER probe 2 GGGAGGAAGGTCGGATCGTTTATTTCAAC 29

PROBE CGATCCGACCTTCCTCCCTCCTCCTCTTCCCTTGGGTCGAACATTGCTCGTCGTCACTGGGTCCTGCTCATATTGGGTTTACAGCTCACATAGGTAGACTTTAGCTTCCCGGGCTCGCAG

120

TARGET GGGCGGGGCGGGGGCGCGAAAGTCTACCTATGTGAGCTGTAAACCCAATATGAGCAGGACCCAGTGACGACGAGCAATGTTCGACCCAAGGGAAGAGGAGGACGCGCCCCCGCCCCGCCC

120

SET OF STAPLES FOR 0SS TETRAHEDRON

0ss1 TGAATCGGTGCCTAATGAGTGAGC 24

0ss2 TAGCCCGGAGGGATAGTGAGTTTCTATGACCCTGTAATAC 40

0ss3 GTTGTACCTATCACCGTACTCAGGAGGTTTAGCCGCCACCGAGAAGCC 48

0ss4 CACCACCCTCATTTTCAATAGGTGAAAAACATGTCACCAG 40

0ss5 AGTGTAAAACGACGGCTCGCAAGACAAAGAACGCGAGAAA 40

0ss6 GTCACGACGTTGTAAAGCCTGGGGCCAACGCGCGGGGAGA 40

SET OF STAPLES FOR 3SS TETRAHEDRON

3ss1 TCGGTGCCTAATGAGTGAGC 20

3ss2 TAGCCCGGAGGGATAGTGAGTTTCTATGACCCTGTA 36

3ss3 TACCTATCACCGTACTCAGGAGGTTTAGCCGCCACCGAGAAGCC 44

3ss4 ACCCTCATTTTCAATAGGTGAAAAACATGTCACCAG 36

3ss5 AGTGTAAAACGACGGCTCGCAAGACAAAGAACGCGA 36

3ss6 CGACGTTGTAAAGCCTGGGGCCAACGCGCGGGGAGA 36

References [S1] Alloyeau, D.;Ding, B.;Ramasse, Q.;Kisielowski, C.;Lee, Z.; Jeon, K.-J. Direct imaging and chemical analysis of unstained DNA origami performed with a

transmission electron microscope. Chemical communications 2011, 47, 9375-9377. [S2] Rafati, A.; Gill, P. Ultrastructural characterizations of DNA nanotubes using scanning tunneling and atomic force microscopes. Journal of Microscopy and

Ultrastructure 2016, 4, 1-5. [S3] Severin, N.;Dorn, M.;Kalachev, A.; Rabe, J. P. Replication of Single Macromolecules with Graphene. Nano letters 2011, 11, 2436-2439. [S4] Moreno-Herrero, F.;Colchero, J.; Baró, A. M. DNA height in scanning force microscopy. Ultramicroscopy 2003, 96, 167-174. [S5] Piantanida, L.;Naumenko, D.;Torelli, E.;Marini, M.;Bauer, D. M.;Fruk, L.;Firrao, G.; Lazzarino, M. Plasmon resonance tuning using DNA origami actuation.

Chem. Commun. 2015, 51, 4789-4792.

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